| Barley(Hordeum vulgare L.)is one of the major cereal grains,which is widely adapted to diverse environmental conditions and is more stress tolerant than wheat and other Triticinae crops.Qingke,a special variety of barley with Tibetan Plateau characteristics,has been used as the major staple food of Tibetans for generations.The adaption to the harsh climatic conditions of the Tibetan Plateau makes it with potential for the genetic improvement of Triticeae crops.SNPs(Single nucleotide polymorphisms)and CNVs(copy number variants)are common types of DNA alterations underlying intra-species genomic variation.They play an important role in contributing to phenotypic variation and overlap loci associated with important traits related to stress adaption.In this study,19 wild barleys from the Levant and Central Asia,27 barley cultivars representative of the globally geographical range of the species,and 44 Qingke germplasms including 8 landraces of more than 100 years old,15 contemporary landraces,13 cultivars and 8 wild Qingkes were used.We compared the genomic variation and genetic diversity within different barley populations from the views of phenotypic variation,SNPs and CNVs.The differential genes between Qingke and other populations,as well as the candidate loci and genes related to phenotypic traits were scanned.And we elucidated the molecular basis of the adaptation to the harsh climatic conditions of the Tibetan Plateau preliminarily.Furthermore,we presented more closely related geographical origins of btr1(Non-brittle rachis 1)and Btr1(brittle rachis 1)alleles and discussed the possible origin of wild Qingke through haplotype analysis in a world core collection of 1,100 barley germplasms.The main results and conclusions are as follows:Phenotyping of 20 agronomic traits showed a coefficient of variation(CV)between5.36%and 59.12%,and a Shannon-Wiener diversity index H’between 1.67 and 2.06 of each phenotypic trait.The traits with narrow genetic variation may be selected as the primary target and fixed by anthropogenic selection during domestication,and the traits with abundant genetic variation may be the result of adaption to diverse habitats.There were significant differences in 9 and 8 traits between different populations of barley and different subpopulations of Qingke,respectively,and there was a significant correlation within most of morphological traits of flag leaf and grain.Principal component analysis revealed that wild barley was characterized by slender grain and leaf,while Qingke was characterized by rounded spherical grain,broad and long leaf,and a higher grain number per panicle due to the six-rowed spike.Cluster analysis indicated that the different phenotypes of Qingke evolved from other barley as a result of the independent geographical isolation and harsh climatic conditions of the Tibetan Plateau.The wide range of variation and the high diversity index of some phenotypic traits of wild barley and Qingke suggested their potential for germplasm improvement of barley cultivars.54,59 and 281 haplotypes were defined in a world core collection of 1,100 barley germplasms for the coding sequences of btr1 and btr2 allele as well as the long segment of Btr1 allele,respectively.The highest Hd andθ_w were observed in South Levant,and the lowest in China.The genetic diversity of wild barley was higher than that of cultivated barley.An excess of rare variants in the wild barley population of South Levant may result from population size expansion,and abundant recent mutations were observed.B1hap268,the haplotype most closely related to that of the btr1-type cultivated barley up to date,was recovered in four accessions originating from a ravine between Jerusalem and Jericho,a town in the northeast of Jerusalem,Israel.Network reconstruction also suggested a plausible ancestral haplotype of wild barley,which was recovered in accessions originating from northern Israel.The haplotype of wild Qingkes(genotype Btr1Btr2)is b1hap13-b2hap04,and that of most cultivated Qingkes(genotype Btr1btr2)is b1hap13-b2hap42.These haplotypes,which may be produced by recombination between btr1-type and btr2-type genotypes,supported a hybridization origin for wild Qingke.A total of 17,067,449 SNP variants were called based on whole-genome resequencing data.The highest SNP density was observed on chromosome 3H,and the lowest on chromosome 1H.Most of the mutations were silent and distributed in the intergenic region.The highest genetic diversity of wild barley in Levant supported the Fertile Crescent as a center of domestication for barley.Six-rowed cultivars displayed a higher level of genetic variation than two-rowed cultivars and the same for wild Qingke vs cultivated Qingke.A high genetic differentiation was observed between Qingke and other germplasms.Population structure analysis indicated a closer relatedness between Qingke and barley cultivars,especially the six-rowed cultivars,and the possible presence of gene flow between wild Qingke and the wild barley in Levant as well as barley cultivars.These results also suggested that wild Qingke originated from hybridization between cultivated Qingke and barley cultivars or wild barley.5,411 candidate genes were screened as differential signals between Qingke and other germplasms by genome-wide scan,accounting for 6.72%of the amount of barley genes,and 75 candidate genes significantly correlated with 4 traits were detected by association analysis,providing great resources for follow-up studies.A total of 85,699 CNV regions with 456.37 Mb in length were identified,accounting for 9.53%of the barley genome.With respect to the counts of CNV regions,the most were observed on chromosome 2H and the least on chromosome 1H,with an average of 10,712per chromosome.With respect to the size of CNV regions,the largest were detected on the chromosome 3H and the smallest on the chromosome 1H,with an average of 57.05 Mb per chromosome.And the number of CNV regions with a size of 2,500 bp was the largest.There were differences in the type,number and size of CNVs in different barley populations.In terms of CN0,wild barley was significantly larger than barley cultivars in number and size.In terms of CN2,wild barley and Qingke were significantly larger than barley cultivars in number,and Qingke was significantly larger than wild barley and then barley cultivars in size.76 CNV regions significantly correlated with 11 traits,which overlapped with 9 genes were detected by association analysis.Furthermore,2,148 CNV regions overlapped with 351annotated genes were screened as differential signals between Qingke and other germplasms,some of which were related to DNA repair or disease resistance.For example,the normal copy number of HORVU3HR1G014630 in Qingke may maintain the ability to remove the UV-induced DNA damage efficiently,while the CNV region insertion in other germplasms may be responsible for the loss of function.Another example was that the increased copy number of disease resistance genes such as HORVU3HR1G082790,HORVU5HR1G017940,and HORVU5HR1G017950 may confer increased resistance to microbial pathogens,which suggested the potential of crop improvement for disease resistance. |
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